Skip to content
Snippets Groups Projects

fix hisat cmd for read pair options

Merged Chelsea Raulerson requested to merge phg_workflow_ps into master
Compare and
1 file
+ 2
2
Preferences
File browser
Compare changes
+ 2
2
@@ -59,9 +59,9 @@ else
module load hisat2/2.1.0-intel
if [ -s difffile ]
then
hisat2 -p $SLURM_CPUS_ON_NODE --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --no-unal --dta -x ${index_path}/hisat_index/genome -U $fq1 -S out.sam --summary-file ${pair_id}.alignerout.txt
hisat2 -p $SLURM_CPUS_ON_NODE --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --no-unal --dta -x ${index_path}/hisat_index/genome -1 $fq1 -2 $fq2 -S out.sam --summary-file ${pair_id}.alignerout.txt
else
hisat2 -p $SLURM_CPUS_ON_NODE --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --no-unal --dta -x ${index_path}/hisat_index/genome -1 $fq1 -2 $fq2 -S out.sam --summary-file ${pair_id}.alignerout.txt
hisat2 -p $SLURM_CPUS_ON_NODE --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --no-unal --dta -x ${index_path}/hisat_index/genome -U $fq1 -S out.sam --summary-file ${pair_id}.alignerout.txt
fi
if [[ $umi==1 ]]
then